Nucleolar dominance is an epigenetic phenomenon that occurs in both the plant and animal kingdoms and describes the transcription of ribosomal RNA genes inherited from one progenitor, but not the other, in an interspecies hybrid or allopolyploid. It has long been thought that dominant genes are selectively activated. However, recent evidence suggests that under-dominant genes are selectively silenced. Cytosine methylation and histone deacetylation are partners in the repression pathway but it is not known if they act in parallel or in series. It is also not clear if chromatin modifications act on the individual rRNA genes, the multi-megabase chromosomal regions where rRNA genes are clustered (NORs), or other regulatory loci. These questions will be addressed using, as our model system, Arabidopsis suecica, an allotetraploid that combines the genomes of A. thaliana and C. arenosa (also known as A. arenosa) In A. suecica, rRNA genes derived from C. arenosa are transcriptionally active and A. thaliana rRNA genes are silenced. To test the hypothesis that cytosine methylation patterns in the progenitor genomes is needed to establish nucleolar dominance, the A. thaliana cytosine hypomethylation mutant ddm1 will be used as one parent to recreate A. suecica lines. The possibility that histone deacetylation causes cytosine demethylation or that cytosine demethylation causes histone hyperacetylation will be examined to test the hypothesis that these chromatin modifications act in series in the control of nucleolar dominance. The hypothesis that rRNA genes are regulated independent of chromosomal location will be tested by determining if rRNA transgenes at ectopic locations are silenced in newly formed A. suecica lines. In a related aim, we will determine if silencing is restricted to the NORs or if it spreads to neighboring genes adjacent to the NORs. These experiments are part of our long-term effort to understand the positive and negative regulatory mechanisms that control rRNA gene transcription. Understanding nucleolar dominance may also shed light on other epigenetic phenomena such as X-chromosome, provirus, and transposable element inactivation or gametic imprinting. Practical benefits may come from such understanding. For instance, derepression of developmentally silenced genes could have potential for rescuing disease phenotypes due to defects in adult-specific paralogs. Our work on nucleolar dominance is expected to contribute new information to our understanding of chromosomal controls of gene expression.